CIMAC - pixel clustering, cell clustering (k=10)
Candace Liu
October 26, 2020
Gaussian blur sigma=2, convert to frequencies before pixel FlowSOM, normalize including calibration channel
Pixel hClusters found using z-score cap=3, k=20, and iterative thresh=2 (1 iteration)
Cell-based clustering using frequencing of 20 hClusters (cap): normalize by size
k=10 for cell clustering
1
Histogram of counts in pixel clusters
2
Heatmaps of pixel clusters x markers
3
Cell-based FlowSOM clustering using 100 pixel clusters
3.1
Cell cluster x frequency of pixel clusters
3.2
Cell cluster x marker (not weighted, segmentation)
3.3
Cell cluster x marker (weighted by pixel cluster frequency)
3.4
Point breakdown
4
Cell-based FlowSOM clustering using hClusters (cap, k=20)
4.1
Cell cluster x frequency of pixel clusters
4.2
Cell cluster x marker (not weighted, segmentation)
4.3
Cell cluster x marker (weighted by pixel cluster frequency)
4.4
Point breakdown